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Testing Departure from Hardy-Weinberg Proportions
Jian Wang1, Sanjay Shete2,3
1Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
Methods in Molecular Biology (Clifton, N.J.)
|October 6, 2017
Summary
The Hardy-Weinberg principle is crucial for population genetics and disease studies. Deviation from its proportions can indicate genetic associations with diseases.
Area of Science:
- Population Genetics
- Human Disease Studies
Background:
- The Hardy-Weinberg principle historically studied allele frequency changes.
- It is now vital for detecting inbreeding, population stratification, and genotyping errors in human disease research.
Purpose of the Study:
- To describe the Hardy-Weinberg principle and its common tests.
- To demonstrate step-by-step applications of chi-squared and exact tests using SAS, R, and PLINK.
- To discuss improved methods for testing Hardy-Weinberg proportions in case-control studies.
Main Methods:
- Comparison of Pearson's chi-squared goodness-of-fit test and the exact test for Hardy-Weinberg proportions.
- Detailed procedural demonstrations using SAS, R, and PLINK software.
- Exploration of advanced testing strategies for case-control designs.
Main Results:
- Pearson's chi-squared test is sensitive to small sample sizes or rare alleles.
- The exact test, via enumeration or Markov chain Monte Carlo, is preferable in such scenarios.
- Deviation from Hardy-Weinberg proportions in affected individuals suggests disease associations.
Conclusions:
- The Hardy-Weinberg principle and its associated tests are fundamental in genetic association studies.
- Software like SAS, R, and PLINK facilitate practical application of these tests.
- Testing for Hardy-Weinberg disequilibrium offers valuable insights into disease-gene associations.
Keywords:
Case–control genetic association studyExact testGenetic association studyGenotyping errorHardy-Weinberg proportionsPLINKPearson’s chi-squared goodness-of-fit testPopulation stratificationQuality controlRSAS/geneticsMore Related Videos
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